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Reduction of inhibitory signaling and selective induction of C-C motif chemokine ligands after spinal cord ischemia

GSE266241 Mus musculus (mouse) RNA-seq (gene expression) 29 samples Submitted 2026/04/30 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 29 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
29 samples: 8 conditions, mostly in triplicateGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Summary (written by the submitters)
We used our mouse model of transient aortic cross clamping (ACC)-induced ischemic spinal cord injury (ISCI) to identify the early molecular changes in the spinal cord (SC) after ACC that contribute to delayed paraplegia in 65-70% of mice. SCs were collected one and four hours (h) after ACC, segmented into cervical and thoracic+lumbar (Th-Lu) sections, and RNA was sequenced.
Read the full summary ↓
The non-ischemic cervical SC was used as control for the 1h post-ACC mice. At 4h, the transcriptome of ACC Th-Lu sections was compared with the transcriptome of sham Th-Lu. The Th-Lu SCs of sham and ACC mice at 4h post–surgery underwent LC-MS/MS phospho-proteomic analysis to identify differentially phosphorylated proteins.At 1h after ACC, transcripts involved in the mitochondrial respirasome electron transport chain (ETC) were downregulated in the ischemic Th-Lu region of the SC. This reduction was paralleled by the induction of pro-inflammatory chemokines Ccl2, Ccl3, and Ccl4, which were further amplified at 4h but only in ~two-thirds of mice. The later increase was paralleled by the downregulation of transcripts encoding post-synaptic membrane proteins, particularly of the GABAergic synapse. Proteins involved in post-synaptic density and synaptic plasticity were found to be hypo-phosphorylated following ISCI. Our data shows that ISCI reduces transcripts for ETC proteins likely leading to a lack of stability in the GABAergic post-synaptic organization and function at 4h. Thus, pharmaceuticals aimed at stabilizing inhibitory synapses may be more effective than excitatory receptor antagonists for alleviating excitotoxicity. On the other hand, the selective induction of Ccl chemokines in a 2:1 ratio of ACC mice (similar to the rate of paralysis at 48h) suggests tight association between intraspinal Ccl induction and paralysis. We posit that combining antagonists for Ccls and/or their receptors with pharmaceuticals aimed at stabilizing GABAergic synapses will be a potent neuroprotective drug regimen after aortic surgery.
This dataset
Open GSE266241 in finder → Find more mouse RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE266241_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1097603 and SRA study SRP500287. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
8 conditions, mostly in triplicate
Thoracic and Lumbar Spinal Cord, Aortic Cross… ×5 Thoracic and Lumbar Spinal Cord, Aortic Cross… ×4 Thoracic and Lumbar Spinal Cord, Sham, 4 hour… ×4 Thoracic and Lumbar Spinal Cord, Sham, 4 hour… ×4 Thoracic and Lumbar Spinal Cord, Aortic Cross… ×3 Thoracic and Lumbar Spinal Cord, Sham, 4 hour… ×3 Thoracic and Lumbar Spinal Cord, Aortic Cross… ×3 Cervical Spinal Cord, Aortic Cross Clamp, 1 h… ×3

Supports a case/control comparison: 4 samples read as cases, 16 as controls.

How we read this: 8 replicated groups read from 29 sample titles; they account for 29 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study
Datasets on a similar topic

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